The Palestinian daily al Quds earlier on Sunday cited Syrian sources who said the Syrian army had targeted an Israeli drone in Quneitra, causing the drone to retreat. Syria claims their missiles downed one Israeli jet and hit another, which Israel rejected as "absolutely untrue".
"The Syrians must understand that they are held responsible for these arms transfers to Hezbollah and that if they continue to allow them then we will do what we have to do".
Syria claimed the planes attacked a Syrian military site, whereas Israel claims it was targeting a shipment of advanced weaponry destined for Hezbollah forces in Lebanon.
"When we identify attempts to transfer advanced weapons to Hezbollah and we have intelligence and it is operationally feasible, we act to prevent it", according to the Times of Israel.
The missiles triggered Israel's emergency sirens, which may have forced the army to issue a rare communique confirming the skirmish.
"At no point was the safety of Israeli civilians or the IAF (Israeli Air Force) aircraft compromised", an Israeli military spokesman said.
Syria said it shot down an Israeli war plane and struck another Friday after four of the aircraft violated Syrian airspace.
Israeli Defense Minister Avigdor Liberman has warned Syria that Israel will destroy its air defense system if Syria fires an anti-aircraft missile at Israeli aircraft again.
A surface-to-air missile (SAM) was intercepted using the Arrow system, created to stop long-range ballistic missiles, reports say.
The Israeli official recognition, which is the first of its kind, also included a statement that the Israeli forces retaliated against a rocket fired from Syria in response to these raids.
Israeli Channel 10 TV reported that Israel deployed its Arrow defence system for the first time against a real threat and hit an incoming missile, intercepting it before it exploded in Israel. The Iran-backed group is sworn to Israel's destruction and fought a month-long war with the Jewish state in 2006.
It comes less than 10 days after the Israeli Prime Minister Benjamin Netanyahu visited Moscow for talks with Vladimir Putin.
Presumably, the two leaders discussed Israel's commitment to defending its northern border against attacks by Hezbollah or Islamic groups in Syria, which now includes ISIS.